Michelle L. Wallander

Comparison of reverse transcription-polymerase chain reaction, immunohistochemistry, and fluorescence in situ hybridization methodologies for detection of echinoderm microtubule-associated proteinlike 4-anaplastic lymphoma kinase fusion-positive non-small cell lung carcinoma: implications for optimal clinical testing.

CONTEXT Echinoderm microtubule-associated proteinlike 4-anaplastic lymphoma kinase (EML4-ALK) gene fusions are detected in 3% to 13% of non-small cell lung carcinomas. Accurate testing for detection of EML4-ALK fusions is essential for appropriate therapy selection. OBJECTIVE To compare reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) methodologies for detection of EML4-ALK fusions. DESIGN Forty-six pulmonary adenocarcinomas were selected with enrichment for wild-type epidermal growth factor receptor (EGFR) status (wild type, n  =  42; mutant, n  =  4). Specimens were tested by IHC (Dako; clone ALK1), FISH (Abbott Molecular; LSI ALK break apart), and RT-PCR (variants 1 and 3a/b). RESULTS EML4-ALK variant 3a/b was detectable by RT-PCR, FISH, and IHC in 4% (2 of 46) of specimens. Complete agreement among FISH and IHC reviewers was obtained for variant 3a/b. No concordance existed among methodologies for the detection of EML4-ALK variant 1. The RT-PCR method detected variant 1 in 20% (9 of 46) of specimens. Agreement among FISH viewers was poor for variant 1 because only 11% (1/9) of specimens were scored as positive by all 3 viewers. The sensitivity of IHC for detection of variant 1 was also poor because only 1 of 9 samples (11%) was scored as positive. Overall, the frequency of EML4-ALK variants 1 and 3a/b was 24% (11 of 46) in adenocarcinomas enriched for wild-type EGFR status. One EML4-ALK variant 1 fusion was found to coexist with an EGFR exon 21 mutation. CONCLUSIONS The FISH interpretation demonstrated great variability among observers. The RT-PCR method was the most sensitive and least-subjective methodology for detection of EML4-ALK fusions.

Cysteine Oxidation Regulates the RNA-Binding Activity of Iron Regulatory Protein 2

ABSTRACT Iron regulatory protein 2 (IRP2) is an RNA-binding protein that regulates the posttranscriptional expression of proteins required for iron homeostasis such as ferritin and transferrin receptor 1. IRP2 RNA-binding activity is primarily regulated by iron-mediated proteasomal degradation, but studies have suggested that IRP2 RNA binding is also regulated by thiol oxidation. We generated a model of IRP2 bound to RNA and found that two cysteines (C512 and C516) are predicted to lie in the RNA-binding cleft. Site-directed mutagenesis and thiol modification show that, while IRP2 C512 and C516 do not directly interact with RNA, both cysteines are located within the RNA-binding cleft and must be unmodified/reduced for IRP2-RNA interactions. Oxidative stress induced by cellular glucose deprivation reduces the RNA-binding activity of IRP2 but not IRP2-C512S or IRP2-C516S, consistent with the formation of a disulfide bond between IRP2 C512 and C516 during oxidative stress. Decreased IRP2 RNA binding is correlated with reduced transferrin receptor 1 mRNA abundance. These studies provide insight into the structural basis for IRP2-RNA interactions and reveal an iron-independent mechanism for regulating iron homeostasis through the redox regulation of IRP2 cysteines.

KIT mutations in ocular melanoma: Frequency and anatomic distribution

KIT mutations are known to occur in ∼15% of chronic sun damaged cutaneous, mucosal, and acral melanomas. Melanomas with demonstrated activating mutations in KIT or platelet-derived growth factor receptor A (PDGFRA) may benefit from treatment with tyrosine kinase inhibitors. Currently, the limited data regarding KIT mutational status in ocular melanoma suggest that activating mutations are extremely rare. PDGFRA mutational status in ocular melanoma has not been determined. Seventy-five ocular melanomas (53 choroidal, 6 iris, 11 ciliary body, and 5 conjuctival) were selected from the files of the Department of Ophthalmology. High-resolution melting curve analysis and sequencing were performed to detect mutations in KIT exons 9, 11, 13, and 17 and PDGFRA exons 12 and 18. Results of mutational analysis were correlated with anatomical site and KIT (CD117) immunohistochemistry. Eight of 75 (11%) ocular melanomas contained mutations in either the KIT or PDGFRA gene. Five of 53 (9%) choroidal melanomas were associated with mutations (KIT exon 11=3; KIT exon 17=1; PDGFRA intron 18=1). Two of six (33%) iris melanomas and a single (9%) ciliary body melanoma harbored KIT exon 11 mutations. No mutations were identified in conjunctival melanomas. The distribution of KIT and PDGFRA mutations by ocular melanoma anatomical site did not reach statistical significance (P=0.393) CD117 positivity was not predictive of KIT mutational status as only 6 of 58 (10%) CD177-positive tumors harbored KIT mutations. In addition, a KIT exon 17 mutation was identified in one CD117-negative tumor. KIT and PDGFRA mutations do occur in ocular melanomas at a frequency (11%) that is similar to acral and mucosal melanomas. Limited correlation of CD117 positivity with mutational status suggests that all ocular melanomas should undergo mutational analysis to determine if imatinib therapy is appropriate.

Iron-independent Phosphorylation of Iron Regulatory Protein 2 Regulates Ferritin during the Cell Cycle

Iron regulatory protein 2 (IRP2) is a key iron sensor that post-transcriptionally regulates mammalian iron homeostasis by binding to iron-responsive elements (IREs) in mRNAs that encode proteins involved in iron metabolism (e.g. ferritin and transferrin receptor 1). During iron deficiency, IRP2 binds IREs to regulate mRNA translation or stability, whereas during iron sufficiency IRP2 is degraded by the proteasome. Here, we identify an iron-independent IRP2 phosphorylation site that is regulated by the cell cycle. IRP2 Ser-157 is phosphorylated by Cdk1/cyclin B1 during G2/M and is dephosphorylated during mitotic exit by the phosphatase Cdc14A. Ser-157 phosphorylation during G2/M reduces IRP2 RNA-binding activity and increases ferritin synthesis, whereas Ser-157 dephosphorylation during mitotic exit restores IRP2 RNA-binding activity and represses ferritin synthesis. These data show that reversible phosphorylation of IRP2 during G2/M has a role in modulating the iron-independent expression of ferritin and other IRE-containing mRNAs during the cell cycle.

Follicular variant of papillary carcinoma: reproducibility of histologic diagnosis and utility of HBME-1 immunohistochemistry and BRAF mutational analysis as diagnostic adjuncts.

ContextDespite the recognition of the follicular variant of papillary carcinoma of the thyroid (FVPTC) for over 50 years, reproducibility of this diagnostic category has remained poor. Architectural features have been of variable utility as some FVPTC seem encapsulated, whereas others are multifocal and may be confused with nodular hyperplasia. Nuclear features are important for diagnosis of FVPTC, but some authors have discounted the utility of nuclear grooves and inclusions. More recently, BRAF and HBME-1 (Human Bone Marrow Endothelial Cell-1) have been suggested as markers for FVPTC. ObjectiveTo investigate the frequency of BRAF mutations and HBME-1 immunopositivity, in a series of FVPTCs in which the diagnosis was established by 100% consensus among a panel of 6 surgical pathologists. DesignTwenty-eight specimens with an original diagnosis of FVPTC and 10 cases with other diagnoses were obtained from the surgical pathology files of the University of Utah School of Medicine. All specimens were independently reviewed by 6 surgical pathologists. Tissue blocks were analyzed for BRAF exon 15 mutations and HMBE-1 expression. ResultsComplete agreement among pathologists for the diagnosis of FVPTC was obtained in 28.6% (8/28) of cases originally diagnosed as FVPTC. Mutations in BRAF exon 15 were found in 25% (2/8) of cases with a 100% consensus diagnosis of FVPTC and 32% (6/19) of cases unanimously diagnosed as a type of papillary carcinoma (classic or follicular variant). HBME-1 was expressed in 87.5% (7/8) of lesions with a 100% consensus diagnosis of FVPTC and 84.2% (16/19) of lesions with a unanimous diagnosis of a type of papillary carcinoma of the thyroid (classic or follicular variant). ConclusionsInterobserver agreement for the diagnosis of FVPTC is poor and testing for the BRAF mutation is only marginally helpful because a minority of FVPTCs possess the mutation. HBME-1 expression when coupled with a BRAF mutation, results in 100% specificity but low sensitivity for the presence of papillary carcinoma of the thyroid including the follicular variant.

MDM2 Amplification in Malignant Peripheral Nerve Sheath Tumors Correlates With p53 Protein Expression

CONTEXT MDM2 is known to be abnormally upregulated in a variety of human neoplasms, secondary to gene amplification. Assessment of MDM2 amplification is most useful clinically for separating lipomas (nonamplified) from atypical lipomatous neoplasms or well-differentiated liposarcomas (amplified). MDM2 amplification occurs in approximately 7% of all human neoplasms. In this study, we sought to determine the utility of MDM2 amplification for the separation of benign (schwannomas) and malignant peripheral nerve sheath tumors (MPNSTs). The expression of p53 was correlated with MDM2 amplification because early studies have indicated that MDM2 is rarely amplified in MPNSTs that express p53. OBJECTIVES To determine the percentage of MPNSTs with MDM2 amplification and the specificity of MDM2 amplification for malignancy in nerve sheath tumors. DESIGN Fifteen MPNSTs, 14 neurofibromas, and 15 schwannomas were obtained from the files of the Department of Pathology. These cases underwent fluorescent in situ hybridization analysis for the presence of MDM2 amplification. Assessments were also made for cellularity (low or high), percentage of cells staining positively for p53 and MDM2 protein, and percentage of cells staining with MIB-1. RESULTS Of 15 MPNSTs, 3 (20%) demonstrated amplification of the MDM2 gene. No neurofibromas or schwannomas demonstrated MDM2 amplification. All 3 MDM2 -amplified MPNSTs were positive for p53. Correlation of MDM2 amplification status and p53 immunoreactivity was statistically significant (P  =  .004). CONCLUSIONS The low frequency (20%) of MDM2 amplification in our series of MPNSTs demonstrates that MDM2 fluorescent in situ hybridization has limited diagnostic value for the separation of benign schwannomas and MPNSTs. Our study demonstrated a positive correlation (P  =  .004) between MDM2 amplification and p53 expression.

Utilization of unlabeled probes for the detection of fibroblast growth factor receptor 2 exons 7 and 12 mutations in endometrial carcinoma.

BackgroundEndometrial adenocarcinomas are associated with a variety of molecular abnormalities including microsatellite instability, Kirsten rat sarcoma viral oncogene homolog mutations, and phosphatase and tensin homolog inactivation. Recently, mutations in fibroblast growth factor receptor 2 (FGFR2) have been described but their frequency and clinicopathologic characteristics are incompletely known. MethodsTo determine the frequency of mutations in FGFR2 exons 7 and 12, 43 adenocarcinomas of the endometrium were studied by high-resolution melting analysis utilizing unlabeled probes and sequencing. ResultsThree of 43 (7%) endometrial carcinomas harbored FGFR2 exon 7 mutations. All 3 mutations were S252W and occurred in endometrioid (type I) adenocarcinomas. Direct sequencing indicated that 2 of the S252W mutations were heterozygous, whereas 1 was presumably homozygous. No FGFR2 mutations were detected in exon 12. ConclusionsFGFR2 mutations occur in approximately 7% of adenocarcinomas of the endometrium. Only carcinomas of an endometrioid morphology contain FGFR2 mutations, and in our series all were S252W. FGFR2 exons 7 and 12 unlabeled DNA probes allow for easy screening of endometrial carcinoma for the 2 most common FGFR2 mutations (S252W and N550K). Identification of these mutations may have important implications in directed molecular therapy.

C-KIT and PDGFRA zygosity in gastrointestinal stromal tumors: Correlation with tumor site, tumor size, exon, and CD117 immunohistochemistry.

BackgroundGastrointestinal stromal tumors (GISTs) often harbor activating mutations in the receptor tyrosine kinases C-KIT or platelet derived growth factor receptor-alpha (PDGFRA). Gain-of-function mutations in these 2 genes, which result in constitutive signaling, are presumed to be dominant and therefore are usually heterozygous. However, homozygous C-KIT mutations have been reported in GISTs, although at varying frequencies in different subsets. MethodsHigh-resolution amplicon melting curve analysis and direct sequencing were used to determine the frequency of mutation zygosity in a series of 267 GIST cases with known C-KIT (exons 9, 11, 13 and 17) or PDGFRA (exons 12 and 18) mutations. Mutation zygosity was correlated with clinicopathological characteristics including sex, age, tumor size, tumor location, and C-KIT immunohistochemistry. ResultsForty-two of 267 (15.7%) mutant GISTs were homozygous: 36 in C-KIT exon 11, 1 in C-KIT exon 13, 2 in PDGFRA exon 12, and 3 in PDGFRA exon 18. No correlation was found between mutation zygosity and age, sex, tumor size, or C-KIT expression. Homozygous mutant GISTs from the small intestine were underrepresented (P=0.029) whereas GISTs from metastatic sites such as the liver or pancreas were significantly enriched for mutant homozygosity (P=0.020). ConclusionsZygosity of C-KIT or PDGFRA mutations did not correlate with most clinicopathologic features of GISTs including tumor size in our subset. However, homozygous mutant GISTs were associated with metastatic disease.

Juvenile granulosa cell tumors: immunoreactivity for CD99 and Fli-1 and EWSR1 translocation status: a study of 11 cases.

The accurate diagnosis of a juvenile granulosa cell tumor (JGCT) can be challenging, as these neoplasms often exhibit morphologic features that overlap other ovarian neoplasms. In addition, the immunohistochemical profile exhibited by JGCT is fairly nonspecific and typically includes reactivity for CD99. Recently, we noted that JGCTs can show immunohistochemical expression of Fli-1, a transcription factor expressed by Ewing sarcoma, a neoplasm that is occasionally in the differential diagnosis of JGCT. We evaluated a series of JGCTs to determine whether Fli-1 is commonly expressed by these tumors and whether they demonstrate chromosomal arrangements in EWSR1. Cases diagnosed as JGCT (n=11) were immunohistochemically evaluated for expression of Fli-1 and CD99. Fluorescence in situ hybridization was performed on all cases to search for chromosomal rearrangements in EWSR1. All 11 of our cases exhibited positive immunohistochemical staining for Fli-1 and CD99. None of the cases demonstrated rearrangement in EWSR1 by fluorescence in situ hybridization. In cases of JGCT that cannot be reliably distinguished from Ewing sarcoma based on morphology and immunohistochemistry alone, fluorescence in situ hybridization testing for EWSR1 rearrangements seems to be a useful diagnostic adjunct for their separation.

Comparison of Dual-ish (dish) With Fluorescence In Situ Hybridization (fish) and Correlation With Immunohistochemical Findings for Her2/neu Status in Breast Carcinoma

Introduction: The most widely used methods for determination of HER2/neu status in breast carcinoma are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Both techniques are associated with technical and interpretive difficulties. Alternative methods exist including quantitative PCR and the newly developed chromogenic dual in situ hybridization (DISH). Methods: We evaluated HER2 DISH as an alternative to FISH and report our findings from 101 cases. In addition, we correlated HER2 DISH and FISH results with HercepTest and 4B5 immunohistochemistry. Results: Eight cases failed FISH analysis and none failed DISH analysis. A 95% (88/93) concordance was found between DISH and FISH for all cases in the series. When only 2+ IHC cases were evaluated, the concordance was 94% for DISH and FISH. Using the 2013 ASCO/CAP recommendations, none of the tested cases were equivocal by FISH or DISH despite 66% of cases being 2+ by HercepTest and 32% by the 4B5 antibody. Comment: Our study, which utilizes a majority of IHC equivocal cases, demonstrates that HER2 FISH and DISH are concordant methodologies. HER2 DISH is therefore an acceptable alternative to FISH.